From 7790148cd12947ecf6e16c2fe72f1c7ac4d0e738 Mon Sep 17 00:00:00 2001
From: Antoine Cyril David Hoffmann <ahoffman@spcpc606.epfl.ch>
Date: Tue, 17 May 2022 15:21:42 +0200
Subject: [PATCH] scripts update
---
matlab/compile_results.m | 113 +++++++++++----------
matlab/compute/compute_fa_1D.m | 4 +-
matlab/compute/compute_fa_2D.m | 4 +-
matlab/compute/mode_growth_meter.m | 155 +++++++++++++++--------------
matlab/plot/plot_fa.m | 8 +-
matlab/plot/plot_fa_gene.m | 14 +--
matlab/plot/plot_metric.m | 26 +++--
wk/analysis_3D.m | 16 +--
wk/analysis_header.m | 3 +-
wk/gene_analysis_3D.m | 25 +++--
10 files changed, 196 insertions(+), 172 deletions(-)
diff --git a/matlab/compile_results.m b/matlab/compile_results.m
index d0892abf..952dec78 100644
--- a/matlab/compile_results.m
+++ b/matlab/compile_results.m
@@ -208,63 +208,68 @@ while(CONTINUE)
JOBNUM = JOBNUM + 1;
end
-%% Build grids
-
-Nky = numel(ky);
-if Nky > 1
- dky = ky(2);
- Ly = 2*pi/dky;
+if(JOBFOUND == 0)
+ disp('no results found, please verify the paths');
+ return;
else
- dky = 0;
- Ly = 0;
-end
-[~,iky0] = min(abs(ky));
-Ny = 2*Nky-1;
-y = linspace(-Ly/2,Ly/2,Ny+1); y = y(1:end-1);
+ %% Build grids
-Nkx = numel(kx);
-if Nkx > 1
- dkx = kx(2);
- Lx = 2*pi/dkx;
-else
- dkx = 0;
- Lx = 0;
-end
-[~,ikx0] = min(abs(kx));
-Nx = Nkx;
-x = linspace(-Lx/2,Lx/2,Nx+1); x = x(1:end-1);
+ Nky = numel(ky);
+ if Nky > 1
+ dky = ky(2);
+ Ly = 2*pi/dky;
+ else
+ dky = 0;
+ Ly = 0;
+ end
+ [~,iky0] = min(abs(ky));
+ Ny = 2*Nky-1;
+ y = linspace(-Ly/2,Ly/2,Ny+1); y = y(1:end-1);
-Nz = numel(z);
+ Nkx = numel(kx);
+ if Nkx > 1
+ dkx = kx(2);
+ Lx = 2*pi/dkx;
+ else
+ dkx = 0;
+ Lx = 0;
+ end
+ [~,ikx0] = min(abs(kx));
+ Nx = Nkx;
+ x = linspace(-Lx/2,Lx/2,Nx+1); x = x(1:end-1);
-[KX,KY] = meshgrid(kx,ky);
-KPERP2 = KX.^2+KY.^2;
-%% Add everything in output structure
-% scaling
-DATA.scale = (1/Nx/Ny)^2;
-% Fields
-DATA.GGAMMA_RI = GGAMMA_; DATA.PGAMMA_RI = PGAMMA_; DATA.HFLUX_X = HFLUX_;
-DATA.Nipj = Nipj_; DATA.Ni00 = Ni00_; DATA.DENS_I = DENS_I_; DATA.TEMP_I = TEMP_I_;
-if(KIN_E)
-DATA.Nepj = Nepj_; DATA.Ne00 = Ne00_; DATA.DENS_E = DENS_E_; DATA.TEMP_E = TEMP_E_;
-end
-DATA.Ts5D = Ts5D_; DATA.Ts3D = Ts3D_; DATA.Ts0D = Ts0D_;
-DATA.PHI = PHI_;
-% grids
-DATA.Pe = Pe; DATA.Pi = Pi;
-DATA.Je = Je; DATA.Ji = Ji;
-DATA.kx = kx; DATA.ky = ky; DATA.z = z;
-DATA.x = x; DATA.y = y;
-DATA.ikx0 = ikx0; DATA.iky0 = iky0;
-DATA.Nx = Nx; DATA.Ny = Ny; DATA.Nz = Nz; DATA.Nkx = Nkx; DATA.Nky = Nky;
-DATA.Pmaxe = numel(Pe); DATA.Pmaxi = numel(Pi); DATA.Jmaxe = numel(Je); DATA.Jmaxi = numel(Ji);
-DATA.dir = DIRECTORY;
-DATA.localdir = DIRECTORY;
-DATA.param_title=['$\nu_{',DATA.CONAME,'}=$', num2str(DATA.NU), ...
- ', $\kappa_N=$',num2str(DATA.K_N),', $L=',num2str(DATA.L),'$, $N=',...
- num2str(DATA.Nx),'$, $(P,J)=(',num2str(DATA.PMAXI),',',...
- num2str(DATA.JMAXI),')$,',' $\mu_{hd}=$(',num2str(DATA.MUx),...
- ',',num2str(DATA.MUy),')'];
-JOBNUM = LASTJOB;
+ Nz = numel(z);
-filename = sprintf([DIRECTORY,'outputs_%.2d.h5'],JOBNUM);
+ [KX,KY] = meshgrid(kx,ky);
+ KPERP2 = KX.^2+KY.^2;
+ %% Add everything in output structure
+ % scaling
+ DATA.scale = (1/Nx/Ny)^2;
+ % Fields
+ DATA.GGAMMA_RI = GGAMMA_; DATA.PGAMMA_RI = PGAMMA_; DATA.HFLUX_X = HFLUX_;
+ DATA.Nipj = Nipj_; DATA.Ni00 = Ni00_; DATA.DENS_I = DENS_I_; DATA.TEMP_I = TEMP_I_;
+ if(KIN_E)
+ DATA.Nepj = Nepj_; DATA.Ne00 = Ne00_; DATA.DENS_E = DENS_E_; DATA.TEMP_E = TEMP_E_;
+ end
+ DATA.Ts5D = Ts5D_; DATA.Ts3D = Ts3D_; DATA.Ts0D = Ts0D_;
+ DATA.PHI = PHI_;
+ % grids
+ DATA.Pe = Pe; DATA.Pi = Pi;
+ DATA.Je = Je; DATA.Ji = Ji;
+ DATA.kx = kx; DATA.ky = ky; DATA.z = z;
+ DATA.x = x; DATA.y = y;
+ DATA.ikx0 = ikx0; DATA.iky0 = iky0;
+ DATA.Nx = Nx; DATA.Ny = Ny; DATA.Nz = Nz; DATA.Nkx = Nkx; DATA.Nky = Nky;
+ DATA.Pmaxe = numel(Pe); DATA.Pmaxi = numel(Pi); DATA.Jmaxe = numel(Je); DATA.Jmaxi = numel(Ji);
+ DATA.dir = DIRECTORY;
+ DATA.localdir = DIRECTORY;
+ DATA.param_title=['$\nu_{',DATA.CONAME,'}=$', num2str(DATA.NU), ...
+ ', $\kappa_N=$',num2str(DATA.K_N),', $L=',num2str(DATA.L),'$, $N=',...
+ num2str(DATA.Nx),'$, $(P,J)=(',num2str(DATA.PMAXI),',',...
+ num2str(DATA.JMAXI),')$,',' $\mu_{hd}=$(',num2str(DATA.MUx),...
+ ',',num2str(DATA.MUy),')'];
+ JOBNUM = LASTJOB;
+
+ filename = sprintf([DIRECTORY,'outputs_%.2d.h5'],JOBNUM);
+end
end
\ No newline at end of file
diff --git a/matlab/compute/compute_fa_1D.m b/matlab/compute/compute_fa_1D.m
index 79fe35d8..e4774f19 100644
--- a/matlab/compute/compute_fa_1D.m
+++ b/matlab/compute/compute_fa_1D.m
@@ -29,12 +29,12 @@ switch options.SPECIE
end
Np = numel(parray); Nj = numel(jarray);
-switch options.Z
+switch options.iz
case 'avg'
Napj_ = mean(Napj_,5);
phi_ = mean(data.PHI,3);
otherwise
- [~,iz] = min(abs(options.Z-data.z));
+ iz = options.iz;
Napj_ = Napj_(:,:,:,:,iz,:);
phi_ = data.PHI(:,:,iz);
end
diff --git a/matlab/compute/compute_fa_2D.m b/matlab/compute/compute_fa_2D.m
index c66ebba5..29a8b093 100644
--- a/matlab/compute/compute_fa_2D.m
+++ b/matlab/compute/compute_fa_2D.m
@@ -26,12 +26,12 @@ switch options.SPECIE
jarray = double(data.Ji);
end
-switch options.Z
+switch options.iz
case 'avg'
Napj_ = mean(Napj_,5);
phi_ = mean(data.PHI,3);
otherwise
- iz = options.Z;
+ iz = options.iz;
Napj_ = Napj_(:,:,:,:,iz,:);
phi_ = data.PHI(:,:,iz);
end
diff --git a/matlab/compute/mode_growth_meter.m b/matlab/compute/mode_growth_meter.m
index d0c1a9ce..b8c229d8 100644
--- a/matlab/compute/mode_growth_meter.m
+++ b/matlab/compute/mode_growth_meter.m
@@ -2,98 +2,99 @@ function [FIGURE] = mode_growth_meter(DATA,OPTIONS)
NORMALIZED = OPTIONS.NORMALIZED;
Nma = OPTIONS.NMA; %Number moving average
-t = OPTIONS.TIME;
+
iz = OPTIONS.iz;
-[~,ikzf] = max(squeeze(mean(abs(squeeze(DATA.PHI(1,:,1,:))),2)));
+[~,ikzf] = max(squeeze(mean(abs(squeeze(DATA.PHI(1,:,iz,:))),2)));
FRAMES = zeros(size(OPTIONS.TIME));
-
for i = 1:numel(OPTIONS.TIME)
[~,FRAMES(i)] =min(abs(OPTIONS.TIME(i)-DATA.Ts3D));
end
+FRAMES = unique(FRAMES);
+t = DATA.Ts3D(FRAMES);
FIGURE.fig = figure; set(gcf, 'Position', [100 100 1200 700])
FIGURE.FIGNAME = 'mode_growth_meter';
for i = 1:2
-MODES_SELECTOR = i; %(1:Zonal, 2: NZonal, 3: ky=kx)
-
-if MODES_SELECTOR == 1
- if NORMALIZED
- plt = @(x,ik) movmean(abs(squeeze(x(1,ik,iz,FRAMES)))./max(abs(squeeze(x(1,ik,iz,FRAMES)))),Nma);
- else
- plt = @(x,ik) movmean(abs(squeeze(x(1,ik,iz,FRAMES))),Nma);
- end
- kstr = 'k_x';
- k = DATA.kx;
- MODESTR = 'Zonal modes';
-elseif MODES_SELECTOR == 2
- if NORMALIZED
- plt = @(x,ik) movmean(abs(squeeze(x(ik,1,iz,FRAMES)))./max(abs(squeeze(x(ik,1,iz,FRAMES)))),Nma);
- else
- plt = @(x,ik) movmean(abs(squeeze(x(ik,1,iz,FRAMES))),Nma);
- end
- kstr = 'k_y';
- k = DATA.ky;
- MODESTR = 'NZ modes';
-elseif MODES_SELECTOR == 3
- if NORMALIZED
- plt = @(x,ik) movmean(abs(squeeze(x(ik,ik,iz,FRAMES)))./max(abs(squeeze(x(ik,ik,iz,FRAMES)))),Nma);
- else
- plt = @(x,ik) movmean(abs(squeeze(x(ik,ik,iz,FRAMES))),Nma);
- end
- kstr = 'k_y=k_x';
- k = DATA.ky;
- MODESTR = 'Diag modes';
-end
+ MODES_SELECTOR = i; %(2:Zonal, 1: NZonal, 3: ky=kx)
-MODES = 1:numel(k);
-% MODES = zeros(size(OPTIONS.K2PLOT));
-% for i = 1:numel(OPTIONS.K2PLOT)
-% [~,MODES(i)] =min(abs(OPTIONS.K2PLOT(i)-k));
-% end
+ if MODES_SELECTOR == 2
+ if NORMALIZED
+ plt = @(x,ik) movmean(abs(squeeze(x(1,ik,iz,FRAMES)))./max(abs(squeeze(x(1,ik,iz,FRAMES)))),Nma);
+ else
+ plt = @(x,ik) movmean(abs(squeeze(x(1,ik,iz,FRAMES))),Nma);
+ end
+ kstr = 'k_x';
+ k = DATA.kx;
+ MODESTR = 'Zonal modes';
+ elseif MODES_SELECTOR == 1
+ if NORMALIZED
+ plt = @(x,ik) movmean(abs(squeeze(x(ik,1,iz,FRAMES)))./max(abs(squeeze(x(ik,1,iz,FRAMES)))),Nma);
+ else
+ plt = @(x,ik) movmean(abs(squeeze(x(ik,1,iz,FRAMES))),Nma);
+ end
+ kstr = 'k_y';
+ k = DATA.ky;
+ MODESTR = 'NZ modes';
+ elseif MODES_SELECTOR == 3
+ if NORMALIZED
+ plt = @(x,ik) movmean(abs(squeeze(x(ik,ik,iz,FRAMES)))./max(abs(squeeze(x(ik,ik,iz,FRAMES)))),Nma);
+ else
+ plt = @(x,ik) movmean(abs(squeeze(x(ik,ik,iz,FRAMES))),Nma);
+ end
+ kstr = 'k_y=k_x';
+ k = DATA.ky;
+ MODESTR = 'Diag modes';
+ end
+ MODES = 1:numel(k);
+ % MODES = zeros(size(OPTIONS.K2PLOT));
+ % for i = 1:numel(OPTIONS.K2PLOT)
+ % [~,MODES(i)] =min(abs(OPTIONS.K2PLOT(i)-k));
+ % end
-% plt = @(x,ik) abs(squeeze(x(1,ik,iz,FRAMES)))./max(abs(squeeze(x(1,ik,iz,FRAMES))));
-gamma = MODES;
-amp = MODES;
-i_=1;
-for ik = MODES
- gr = polyfit(t',log(plt(DATA.PHI,ik)),1);
- gamma(i_) = gr(1);
- amp(i_) = gr(2);
- i_=i_+1;
-end
+ % plt = @(x,ik) abs(squeeze(x(1,ik,iz,FRAMES)))./max(abs(squeeze(x(1,ik,iz,FRAMES))));
-%plot
-subplot(2,3,1+3*(i-1))
- [YY,XX] = meshgrid(t,fftshift(k,1));
- pclr = pcolor(XX,YY,abs(plt(fftshift(DATA.PHI,MODES_SELECTOR),1:numel(k))));set(pclr, 'edgecolor','none'); hold on;
- set(gca,'YDir','normal')
-% xlim([t(1) t(end)]); %ylim([1e-5 1])
- xlabel(['$',kstr,'\rho_s$']); ylabel('$t c_s /\rho_s$');
- title(MODESTR)
-
-subplot(2,3,2+3*(i-1))
- mod2plot = [2:OPTIONS.NMODES+1];
- for i_ = mod2plot
- semilogy(t,plt(DATA.PHI,MODES(i_))); hold on;
-% semilogy(t,exp(gamma(i_).*t+amp(i_)),'--k')
- end
- if MODES_SELECTOR == 1
- semilogy(t,plt(DATA.PHI,ikzf),'--k');
- end
- xlim([t(1) t(end)]); %ylim([1e-5 1])
- xlabel('$t c_s /\rho_s$'); ylabel(['$|\phi_{',kstr,'}|$']);
- title('Measure time window')
-
-subplot(2,3,3+3*(i-1))
- plot(k(MODES),gamma); hold on;
- plot(k(MODES(mod2plot)),gamma(mod2plot),'x')
- if MODES_SELECTOR == 1
- plot(k(ikzf),gamma(ikzf),'ok');
+ gamma = MODES;
+ amp = MODES;
+ i_=1;
+ for ik = MODES
+ gr = polyfit(t,log(plt(DATA.PHI,ik)),1);
+ gamma(i_) = gr(1);
+ amp(i_) = gr(2);
+ i_=i_+1;
end
- xlabel(['$',kstr,'\rho_s$']); ylabel('$\gamma$');
- title('Growth rates')
+
+ %plot
+ subplot(2,3,1+3*(i-1))
+ [YY,XX] = meshgrid(t,fftshift(k));
+ pclr = pcolor(XX,YY,abs(plt(fftshift(DATA.PHI,MODES_SELECTOR),1:numel(k))));set(pclr, 'edgecolor','none'); hold on;
+ set(gca,'YDir','normal')
+ % xlim([t(1) t(end)]); %ylim([1e-5 1])
+ xlabel(['$',kstr,'\rho_s$']); ylabel('$t c_s /\rho_s$');
+ title(MODESTR)
+
+ subplot(2,3,2+3*(i-1))
+ mod2plot = [2:OPTIONS.NMODES+1];
+ for i_ = mod2plot
+ semilogy(t,plt(DATA.PHI,MODES(i_))); hold on;
+ % semilogy(t,exp(gamma(i_).*t+amp(i_)),'--k')
+ end
+ if MODES_SELECTOR == 2
+ semilogy(t,plt(DATA.PHI,ikzf),'--k');
+ end
+ xlim([t(1) t(end)]); %ylim([1e-5 1])
+ xlabel('$t c_s /\rho_s$'); ylabel(['$|\phi_{',kstr,'}|$']);
+ title('Measure time window')
+
+ subplot(2,3,3+3*(i-1))
+ plot(k(MODES),gamma); hold on;
+ plot(k(MODES(mod2plot)),gamma(mod2plot),'x')
+ if MODES_SELECTOR == 2
+ plot(k(ikzf),gamma(ikzf),'ok');
+ end
+ xlabel(['$',kstr,'\rho_s$']); ylabel('$\gamma$');
+ title('Growth rates')
end
end
\ No newline at end of file
diff --git a/matlab/plot/plot_fa.m b/matlab/plot/plot_fa.m
index 00a2ca2f..efdbd15f 100644
--- a/matlab/plot/plot_fa.m
+++ b/matlab/plot/plot_fa.m
@@ -1,11 +1,11 @@
function [ FIGURE ] = plot_fa( DATA, OPTIONS )
FIGURE.fig = figure; FIGURE.FIGNAME = ['f_a_',DATA.PARAMS];
-switch OPTIONS.Z
+switch OPTIONS.iz
case 'avg'
zcomp = ' z-avg';
otherwise
- zcomp = [' z=',sprintf('%2.2f',DATA.z(OPTIONS.Z))];
+ zcomp = [' z=',sprintf('%2.2f',DATA.z(OPTIONS.iz))];
end
if OPTIONS.ONED
[s,x,fsa,fxa] = compute_fa_1D(DATA, OPTIONS);
@@ -13,12 +13,12 @@ if OPTIONS.ONED
subplot(1,2,1)
plot(s,fsa); hold on
legend(OPTIONS.SPECIE)
- xlabel('$v_\parallel, (\mu=0)$'); ylabel('$\langle |f_a|^2\rangle_{xy}^{1/2}$');
+ xlabel('$v_\parallel, (\mu=0)$'); ylabel(['$\langle |f_a|^2\rangle_{xy}^{1/2}$, ',zcomp]);
title(DATA.param_title);
subplot(1,2,2)
plot(x,fxa); hold on;
legend(OPTIONS.SPECIE)
- xlabel('$\mu, (v_\parallel=0)$'); ylabel('$\langle |f_a|^2\rangle_{xy}^{1/2}$');
+ xlabel('$\mu, (v_\parallel=0)$'); ylabel(['$\langle |f_a|^2\rangle_{xy}^{1/2}$, ',zcomp]);
if numel(it) == 1
title(['t=',num2str(DATA.Ts5D(it))]);
else
diff --git a/matlab/plot/plot_fa_gene.m b/matlab/plot/plot_fa_gene.m
index 997cfe1f..9792d557 100644
--- a/matlab/plot/plot_fa_gene.m
+++ b/matlab/plot/plot_fa_gene.m
@@ -10,13 +10,13 @@ mu = h5read([folder,file],'/coord/mu'); nmu = numel(mu);
z = h5read([folder,file],'/coord/z');
[XX,SS] = meshgrid(mu,vp);
-switch OPTIONS.Z
+switch OPTIONS.iz
case 'avg'
zcomp_name = ' z-avg';
zcomp = @(x) squeeze(mean(x,1));
otherwise
- zcomp_name = [' z=',sprintf('%2.2f',z(OPTIONS.Z))];
- zcomp = @(x) squeeze(x(OPTIONS.Z,:,:));
+ zcomp_name = [' z=',sprintf('%2.2f',z(OPTIONS.iz))];
+ zcomp = @(x) squeeze(x(OPTIONS.iz,:,:));
end
[~,iv0] = min(abs(vp));
@@ -40,14 +40,14 @@ Gdata = Gdata ./ numel(TIMES);
if OPTIONS.ONED
switch specie
case 'e'
- FFa = squeeze(Gdata(1,:,:,2));
+ FFa = zcomp(Gdata(:,:,:,2));
FFa = abs(FFa)./max(max(abs(FFa)));
subplot(1,2,1)
plot(vp,FFa(:,im0)); hold on;
subplot(1,2,2)
plot(mu,FFa(iv0,:)); hold on;
case 'i'
- FFa = squeeze(Gdata(1,:,:,1));
+ FFa = zcomp(Gdata(:,:,:,1));
FFa = abs(FFa)./max(max(abs(FFa)));
end
@@ -64,7 +64,7 @@ else
switch specie
case 'e'
name = '$f_e(v_\parallel,\mu_p)$';
- FFa = zcomp(squeeze(Gdata));
+ FFa = zcomp(squeeze(Gdata(:,:,:,2)));
FFa = abs(FFa)./max(max(abs(FFa)));
switch PLT_FCT
case 'contour'
@@ -76,7 +76,7 @@ switch specie
end
case 'i'
name = '$f_i(v_\parallel,\mu_p)$';
- FFa = zcomp(squeeze(Gdata));
+ FFa = zcomp(squeeze(Gdata(:,:,:,1)));
FFa = abs(FFa)./max(max(abs(FFa)));
switch PLT_FCT
case 'contour'
diff --git a/matlab/plot/plot_metric.m b/matlab/plot/plot_metric.m
index b4b9e080..7b95c932 100644
--- a/matlab/plot/plot_metric.m
+++ b/matlab/plot/plot_metric.m
@@ -1,25 +1,29 @@
function [ fig ] = plot_metric( data )
-names = {'$g^{xx}$','$g^{xy}$','$g^{xz}$','$g^{yy}$','$g^{yz}$','$g^{zz}$',...
- '$B_0$','$\partial_x B_0$','$\partial_y B_0$','$\partial_z B_0$',...
- '$J$','$R$','$\phi$','$Z$','$\partial_R x$','$\partial_Z x$'};
-data.geo_arrays = load([data.localdir,'geometry.dat']);
+names = {'Jacobian','gradxB','gradyB','gradzB','gradz_coeff',...
+ 'gxx','gxy','gyy','gyz','gzz','hatB','hatR','hatZ'};
+geo_arrays = zeros(2,data.Nz,numel(names));
+
+for i_ = 1:numel(names)
+ namae = names{i_};
+ geo_arrays(:,:,i_) = h5read(data.outfilenames{end},['/data/metric/',namae])';
+end
fig = figure;
subplot(311)
- for i = 1:6
- plot(data.z, data.geo_arrays(:,i),'DisplayName',names{i}); hold on;
+ for i = 1:5
+ plot(data.z, geo_arrays(1,:,i),'DisplayName',names{i}); hold on;
end
xlim([min(data.z),max(data.z)]); legend('show'); title('MoNoLiT geometry');
-
+
subplot(312)
- for i = 7:10
- plot(data.z, data.geo_arrays(:,i),'DisplayName',names{i}); hold on;
+ for i = 6:10
+ plot(data.z, geo_arrays(1,:,i),'DisplayName',names{i}); hold on;
end
xlim([min(data.z),max(data.z)]); legend('show');
subplot(313)
- for i = 11:16
- plot(data.z, data.geo_arrays(:,i),'DisplayName',names{i}); hold on;
+ for i = 11:13
+ plot(data.z, geo_arrays(1,:,i),'DisplayName',names{i}); hold on;
end
xlim([min(data.z),max(data.z)]); legend('show');
end
diff --git a/wk/analysis_3D.m b/wk/analysis_3D.m
index 0b8fef01..e9ab6b17 100644
--- a/wk/analysis_3D.m
+++ b/wk/analysis_3D.m
@@ -10,7 +10,7 @@ system(['mkdir -p ',MISCDIR]);
CMD = ['rsync ', LOCALDIR,'outputs* ',MISCDIR]; disp(CMD);
system(CMD);
% Load outputs from jobnummin up to jobnummax
-JOBNUMMIN = 00; JOBNUMMAX = 10;
+JOBNUMMIN = 00; JOBNUMMAX = 08;
data = compile_results(MISCDIR,JOBNUMMIN,JOBNUMMAX); %Compile the results from first output found to JOBNUMMAX if existing
@@ -53,7 +53,7 @@ options.PLAN = 'xy';
% options.PLAN = 'sx';
options.COMP = 9;
% options.TIME = dat.Ts5D;
-options.TIME = 900:1:990;
+options.TIME = 920:1:1250;
data.EPS = 0.1;
data.a = data.EPS * 2000;
create_film(data,options,'.gif')
@@ -99,9 +99,9 @@ if 0
% options.XPERP = linspace( 0,6,64);
options.SPAR = gene_data.vp';
options.XPERP = gene_data.mu';
-options.Z = 'avg';
-options.T = 900;
-options.PLT_FCT = 'contour';
+options.iz = 13;
+options.T = 20;
+options.PLT_FCT = 'pcolor';
options.ONED = 0;
options.non_adiab = 1;
options.SPECIE = 'i';
@@ -164,10 +164,10 @@ if 0
%% Mode evolution
options.NORMALIZED = 1;
options.K2PLOT = 1;
-options.TIME = 5:1:15;
+options.TIME = 2:20;
options.NMA = 1;
-options.NMODES = 5;
-options.iz = 1;
+options.NMODES = 15;
+options.iz = 9;
fig = mode_growth_meter(data,options);
save_figure(data,fig)
end
diff --git a/wk/analysis_header.m b/wk/analysis_header.m
index a97d0de7..3ff76bdc 100644
--- a/wk/analysis_header.m
+++ b/wk/analysis_header.m
@@ -6,7 +6,8 @@ outfile ='';
outfile ='';
outfile ='';
% outfile ='shearless_cyclone/128x128x16xdmax_6_L_120_CBC_1.0';
-outfile ='shearless_cyclone/128x128x16xdmax_L_120_CBC_1.0';
+% outfile ='shearless_cyclone/128x128x16xdmax_L_120_CBC_1.0';
+outfile ='shearless_cyclone/linear_CBC_120';
% outfile ='quick_run/CLOS_1_64x64_5x3_L_120_kN_2.0_kT_0.5_nu_1e-01_SGGK';
% outfile ='pedestal/64x64x16x2x1_L_300_LnT_20_nu_0.1';
% outfile ='quick_run/32x32x16_5x3_L_300_q0_2.5_e_0.18_kN_20_kT_20_nu_1e-01_DGGK';
diff --git a/wk/gene_analysis_3D.m b/wk/gene_analysis_3D.m
index 5f83d870..31652e6e 100644
--- a/wk/gene_analysis_3D.m
+++ b/wk/gene_analysis_3D.m
@@ -1,6 +1,7 @@
% folder = '/misc/gene_results/shearless_cyclone/miller_output_1.0/';
% folder = '/misc/gene_results/shearless_cyclone/miller_output_0.8/';
-folder = '/misc/gene_results/shearless_cyclone/s_alpha_output_1.0/';
+% folder = '/misc/gene_results/shearless_cyclone/s_alpha_output_1.0/';
+folder = '/misc/gene_results/shearless_cyclone/linear_s_alpha_CBC_100/';
% folder = '/misc/gene_results/shearless_cyclone/s_alpha_output_0.5/';
% folder = '/misc/gene_results/shearless_cyclone/LD_s_alpha_output_1.0/';
% folder = '/misc/gene_results/shearless_cyclone/LD_s_alpha_output_0.8/';
@@ -30,11 +31,11 @@ options.NAME = '\phi';
% options.NAME = 'T_i';
% options.NAME = '\Gamma_x';
% options.NAME = 'k^2n_e';
-options.PLAN = 'xy';
+options.PLAN = 'kxky';
% options.NAME ='f_e';
% options.PLAN = 'sx';
options.COMP = 'avg';
-options.TIME = [500];
+options.TIME = [0 500];
gene_data.a = data.EPS * 2000;
fig = photomaton(gene_data,options);
save_figure(gene_data,fig)
@@ -50,7 +51,7 @@ options.NAME = '\phi';
% options.NAME = 'n_i^{NZ}';
% options.NAME = '\Gamma_x';
% options.NAME = 'n_i';
-options.PLAN = 'kxky';
+options.PLAN = 'xy';
% options.NAME = 'f_e';
% options.PLAN = 'sx';
options.COMP = 'avg';
@@ -91,9 +92,21 @@ options.times = 200:600;
options.specie = 'i';
options.PLT_FCT = 'pcolor';
options.folder = folder;
-options.Z = 'avg';
+options.iz = 1;
options.FIELD = '<f_>';
-options.ONED = 1;
+options.ONED = 0;
% options.FIELD = 'Q_es';
plot_fa_gene(options);
end
+
+if 0
+%% Mode evolution
+options.NORMALIZED = 1;
+options.K2PLOT = 1;
+options.TIME = 50:150;
+options.NMA = 1;
+options.NMODES = 5;
+options.iz = 9;
+fig = mode_growth_meter(gene_data,options);
+save_figure(data,fig)
+end
\ No newline at end of file
--
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